A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human Health
A functional readout of the gut microbiome is necessary to enable precise control of the gut microbiome’s functions, which support human health and prevent or minimize a wide range of chronic diseases. Stool metatranscriptomic analysis offers a comprehensive functional view of the gut microbiome, bu...
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| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2019-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2019/1718741 |
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| author | Andrew Hatch James Horne Ryan Toma Brittany L. Twibell Kalie M. Somerville Benjamin Pelle Kinga P. Canfield Matvey Genkin Guruduth Banavar Ally Perlina Helen Messier Niels Klitgord Momchilo Vuyisich |
| author_facet | Andrew Hatch James Horne Ryan Toma Brittany L. Twibell Kalie M. Somerville Benjamin Pelle Kinga P. Canfield Matvey Genkin Guruduth Banavar Ally Perlina Helen Messier Niels Klitgord Momchilo Vuyisich |
| author_sort | Andrew Hatch |
| collection | DOAJ |
| description | A functional readout of the gut microbiome is necessary to enable precise control of the gut microbiome’s functions, which support human health and prevent or minimize a wide range of chronic diseases. Stool metatranscriptomic analysis offers a comprehensive functional view of the gut microbiome, but despite its usefulness, it has rarely been used in clinical studies due to its complexity, cost, and bioinformatic challenges. This method has also received criticism due to potential intrasample variability, rapid changes, and RNA degradation. Here, we describe a robust and automated stool metatranscriptomic method, called Viomega, which was specifically developed for population-scale studies. Viomega includes sample collection, ambient temperature sample preservation, total RNA extraction, physical removal of ribosomal RNAs (rRNAs), preparation of directional Illumina libraries, Illumina sequencing, taxonomic classification based on a database of >110,000 microbial genomes, and quantitative microbial gene expression analysis using a database of ~100 million microbial genes. We applied this method to 10,000 human stool samples and performed several small-scale studies to demonstrate sample stability and consistency. In summary, Viomega is an inexpensive, high-throughput, automated, and accurate sample-to-result stool metatranscriptomic technology platform for large-scale studies and a wide range of applications. |
| format | Article |
| id | doaj-art-c8604d38b0d64ed8ada94fb02899be6e |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2019-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-c8604d38b0d64ed8ada94fb02899be6e2025-02-03T01:10:23ZengWileyInternational Journal of Genomics2314-436X2314-43782019-01-01201910.1155/2019/17187411718741A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human HealthAndrew Hatch0James Horne1Ryan Toma2Brittany L. Twibell3Kalie M. Somerville4Benjamin Pelle5Kinga P. Canfield6Matvey Genkin7Guruduth Banavar8Ally Perlina9Helen Messier10Niels Klitgord11Momchilo Vuyisich12Viome Inc., Los Alamos, NM 87544, USAViome Inc., Los Alamos, NM 87544, USAViome Inc., Los Alamos, NM 87544, USAViome Inc., Los Alamos, NM 87544, USAViome Inc., Los Alamos, NM 87544, USAViome Inc., Los Alamos, NM 87544, USAViome Inc., Los Alamos, NM 87544, USAViome Inc., Los Alamos, NM 87544, USAViome Inc., Los Alamos, NM 87544, USAViome Inc., Los Alamos, NM 87544, USAViome Inc., Los Alamos, NM 87544, USAViome Inc., Los Alamos, NM 87544, USAViome Inc., Los Alamos, NM 87544, USAA functional readout of the gut microbiome is necessary to enable precise control of the gut microbiome’s functions, which support human health and prevent or minimize a wide range of chronic diseases. Stool metatranscriptomic analysis offers a comprehensive functional view of the gut microbiome, but despite its usefulness, it has rarely been used in clinical studies due to its complexity, cost, and bioinformatic challenges. This method has also received criticism due to potential intrasample variability, rapid changes, and RNA degradation. Here, we describe a robust and automated stool metatranscriptomic method, called Viomega, which was specifically developed for population-scale studies. Viomega includes sample collection, ambient temperature sample preservation, total RNA extraction, physical removal of ribosomal RNAs (rRNAs), preparation of directional Illumina libraries, Illumina sequencing, taxonomic classification based on a database of >110,000 microbial genomes, and quantitative microbial gene expression analysis using a database of ~100 million microbial genes. We applied this method to 10,000 human stool samples and performed several small-scale studies to demonstrate sample stability and consistency. In summary, Viomega is an inexpensive, high-throughput, automated, and accurate sample-to-result stool metatranscriptomic technology platform for large-scale studies and a wide range of applications.http://dx.doi.org/10.1155/2019/1718741 |
| spellingShingle | Andrew Hatch James Horne Ryan Toma Brittany L. Twibell Kalie M. Somerville Benjamin Pelle Kinga P. Canfield Matvey Genkin Guruduth Banavar Ally Perlina Helen Messier Niels Klitgord Momchilo Vuyisich A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human Health International Journal of Genomics |
| title | A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human Health |
| title_full | A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human Health |
| title_fullStr | A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human Health |
| title_full_unstemmed | A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human Health |
| title_short | A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human Health |
| title_sort | robust metatranscriptomic technology for population scale studies of diet gut microbiome and human health |
| url | http://dx.doi.org/10.1155/2019/1718741 |
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